4E9M

NOD1 card domain with three disulfide-clinched, domain-swapped dimers in the asymmetric unit

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CARD	e4e9mA1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
B	CARD	e4e9mB3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
C	CARD	e4e9mC3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
D	CARD	e4e9mD3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
E	CARD	e4e9mE3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
F	CARD	e4e9mF3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
B	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
C	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
D	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
E	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
F	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00619	Caspase recruitment domain (CARD)	Caspase recruitment domain	Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (Pfam:PF00531) domain-like fold .	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Nucleotide-binding oligomerization domain-containing protein 1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein-containing complex binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity cysteine-type endopeptidase activator activity involved in apoptotic process molecular function regulator activity cysteine-type endopeptidase regulator activity involved in apoptotic process peptidase activator activity peptidase activator activity involved in apoptotic process identical protein binding protein binding glycosaminoglycan binding peptidoglycan binding ubiquitin binding ubiquitin-like protein binding molecular transducer activity pattern recognition receptor activity signaling receptor activity protein homodimerization activity protein dimerization activity CARD domain binding protein domain specific binding	cellular process apoptotic process cell death programmed cell death cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process cellular process apoptotic process cell death programmed cell death cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process immune response response to other organism regulation of innate immune response response to external stimulus regulation of response to stimulus defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response response to external biotic stimulus nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway positive regulation of innate immune response nucleotide-binding oligomerization domain containing 1 signaling pathway defense response biological regulation defense response to symbiont immune system process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular process detection of external biotic stimulus detection of biotic stimulus detection of bacterium detection of stimulus response to bacterium detection of other organism defense response to bacterium catabolic process macroautophagy cellular metabolic process autophagy xenophagy cellular catabolic process metabolic process process utilizing autophagic mechanism multicellular organismal process interleukin-1 production cellular biosynthetic process positive regulation of cellular metabolic process regulation of interleukin-1 beta production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of interleukin-1 beta production organic substance metabolic process positive regulation of biosynthetic process regulation of cytokine production organic substance biosynthetic process cytokine production regulation of multicellular organismal process positive regulation of interleukin-1 production positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of interleukin-1 production regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process interleukin-1 beta production positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process positive regulation of cellular biosynthetic process positive regulation of xenophagy regulation of autophagy positive regulation of macroautophagy positive regulation of autophagy regulation of xenophagy regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy regulation of cellular catabolic process positive regulation of cellular catabolic process positive regulation of interleukin-8 production interleukin-8 production regulation of interleukin-8 production positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication positive regulation of signaling positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of molecular function organic cyclic compound metabolic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process regulation of DNA-templated transcription defense response to Gram-negative bacterium regulation of immune effector process regulation of cytokine production involved in immune response immune effector process regulation of macrophage cytokine production positive regulation of production of molecular mediator of immune response regulation of production of molecular mediator of immune response positive regulation of macrophage cytokine production positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of immune effector process myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response positive regulation of cytokine production involved in immune response macrophage cytokine production cellular response to stress response to endoplasmic reticulum stress positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction regulation of catalytic activity positive regulation of protein metabolic process positive regulation of peptidase activity positive regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of proteolysis proteolysis regulation of endopeptidase activity protein metabolic process activation of cysteine-type endopeptidase activity involved in apoptotic process regulation of cysteine-type endopeptidase activity organonitrogen compound metabolic process regulation of protein metabolic process regulation of peptidase activity positive regulation of catalytic activity positive regulation of hydrolase activity positive regulation of cysteine-type endopeptidase activity regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis positive regulation of ERK1 and ERK2 cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production cellular response to nitrogen compound response to organic substance response to organonitrogen compound response to endogenous stimulus response to oxygen-containing compound cellular response to muramyl dipeptide response to muramyl dipeptide response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to organonitrogen compound response to chemical cellular response to organic substance regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction inflammatory response regulation of dendritic cell antigen processing and presentation positive regulation of dendritic cell antigen processing and presentation positive regulation of antigen processing and presentation antigen processing and presentation regulation of antigen processing and presentation dendritic cell antigen processing and presentation regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production defense response to Gram-positive bacterium	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery basal part of cell membrane plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane apical part of cell apical plasma membrane membrane-bounded organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery basal part of cell membrane plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane apical part of cell apical plasma membrane membrane-bounded organelle intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle vesicle endocytic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001611	Leucine-rich repeat	Repeat
A, B, C, D, E A, B, C, D, E, F	IPR041075	NOD2, winged helix domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR007111	NACHT nucleoside triphosphatase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR041267	NACHT, LRR and PYD domains-containing protein, helical domain HD2	Domain
A, B, C, D, E A, B, C, D, E, F	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001315	CARD domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: Q9Y239	nervous system disorder glioblastoma inflammatory bowel disease subependymal giant cell astrocytoma lung carcinoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.